GENESIS: Documentation

Related Documentation:
GENESIS System

Developer Installation Ubuntu (Lucid)

Installing GENESIS on Ubuntu requires executing the following major steps. Note: Installation requires administrator privileges.

• Prepare and upgrade the system software.
• Download and install the DeveloperPackage.
• Install the software packages.
• Check if the installation was successful.

Prepare and upgrade the system software

• Install the following packages using the Start Menu -> System Settings -> Add and Remove Software -> Software Management menu. Always follow the option to install additional dependencies.
  • libyaml-perl
  • libexpect-perl
  • libinline-perl
  • libfile-find-rule-perl
  • libdigest-sha-perl
  • libdevel-ptkdb-perl
  • autoconf
  • automake
  • libc6-dev
  • libncurses5-dev
  • flex
  • bison
  • libperl-dev
  • patch
  • python-dev
  • python-yaml
  • swig
  • libreadline5-dev
  • libclone-perl
  • libterm-readline-gnu-perl
  • libxml-simple-perl
  • latex2rtf
  • biblatex
  • tex4ht
  • monotone

Download and Install the DeveloperPackage

1. Download the latest version of the DeveloperPackage, available from the GENESIS package archive. It is called developer-release-label.tar.gz, where release-label is the current release identifier.
2. Change to the directory where you downloaded the file.
3. Unpack the archive by typing “tar xfz developer-release-label.tar.gz”.
4. Change to the directory with the content of the archive by typing “cd developer-release-label”.
5. Configure by typing “./configure”. If this step fails, it is likely due missing dependencies. If you let us know what dependencies were missing for you, we can update this page, and avoid installation problems for other people.
6. Compile by typing “make”.
7. Install by typing “sudo make install”.

Install software packages

1. Use the installer script to create the correct directory layout by typing “neurospaces_create_directories”.
2. Pull the archives of the source code by typing “neurospaces_pull”.
3. Update the source code in the working directories by typing “neurospaces_update”.
4. Generate make files by typing “neurospaces_configure”.
5. Compile and install the software by typing “neurospaces_install”.

Check if the installation was successful

This step is optional but strongly advised.

• Run tests of all the packages and save tester output to a file by typing “neurospaces_check >/tmp/check.out 2>&1”.
• Check the output by typing “less /tmp/check.out”. Importantly, search for lines containing the string error_count.

Optional Dependencies

G-Tube

As the G-Tube is becoming more mature as the official G-3 GUI, it is strongly recommended that you also install the dependencies of the G-Tube:

• mercurial
• python-numpy
• python-wxtools
• python-wxgtk2.8
• python-wxglade

Studio

The following packages can optionally be installed to run the graphical part of the Studio:

• libgtk2-perl
• libgraphviz-perl
• sdl-perl
• xaw3dg

After successful installation of the Studio, issue the shell command “neurospaces cells/purkinje/edsjb1994.ndf --gui” to check that the graphical component works correctly.